Hi,
I am new at using the Bio::TreeIO module specifically using the newick
format for a phylogenetic analysis. The sample_tree attached is
Newick-formatted tree. My objective is to get all the distances between all
the leaf nodes. I copied examples of the code from
http://www.bioperl.org/wiki/HOWTO:Trees but it does not tell me much (to my
knowledge) so that I understand how to assign the right array value for the
nodes/leaves. The message would say must provide 2 root nodes.
Here is what I have right now:
#!/usr/bin/perl -w
use strict;
my $treefile = 'sample_tree';
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => $treefile);
while (my $tree = $treeio->next_tree) {
my @leaves = $tree->get_leaf_nodes;
for (my $dist = $tree->distance(-nodes => \@leaves)){
print "Distance between trees is $dist\n";
}
}
Thanks,
Jeff
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